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tools for working with genome variation graphs
https://biostars.org/tag/vg/
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VG crashed when performing construct #2048

Open tahuh opened 5 years ago

tahuh commented 5 years ago

Please describe: Hi

I'm trying subcommand "construct" using reference sequence VCF files that I using is COSMIC's coding/non-coding variants from COSMIC v87 data and dbSNP 150 Also I tried using insertion sequence list from those VCF files. The command I used is shown below

vg construct -r /Data/reference/hg38.fa -v /Data/reference/CosmicCodingMuts_v87.vcf -v /Data/reference/CosmicNonCodingVariants_v87.vcf -v /Data/reference/dbsnp150.vcf.gz -I /Data/reference/hg38_vg_insersion_cosmic_coding_non_coding_dbsnp150.fa > hg38.vg

The error message vg sent me is written below

vg: src/constructor.cpp:2041: void vg::Constructor::construct_graph(const std::vector<FastaReference*>&, const std::vector<vcflib::VariantCallFile*>&, const std::vector<FastaReference*>&, std::function<void(vg::Graph&)>): Assertion `reference_for.count(fasta_contig)' failed.
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_ktaDns/stacktrace.txt

Error stack is shown below

Crash report for vg v1.12.1-113-g5c08133 "Parolise"
Stack trace (most recent call last):
#10   Object "", at 0xffffffffffffffff, in 
#9    Object "/Data/program/vg/bin/vg", at 0x792c18, in _start
#8    Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46dfe82f, in __libc_start_main
      Source "../csu/libc-start.c", line 291, in __libc_start_main [0x7ffa46dfe82f]
#7    Object "/Data/program/vg/bin/vg", at 0x6dc48b, in main
      Source "src/main.cpp", line 68, in main [0x6dc48b]
#6    Object "/Data/program/vg/bin/vg", at 0xbb2937, in vg::subcommand::Subcommand::operator()(int, char**) const
    | Source "src/subcommand/subcommand.cpp", line 72, in operator()
      Source "/usr/include/c++/5/functional", line 2267, in operator() [0xbb2937]
       2264:     {
       2265:       if (_M_empty())
       2266:    __throw_bad_function_call();
      >2267:       return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...);
       2268:     }
       2269: 
       2270: #if __cpp_rtti
#5    Object "/Data/program/vg/bin/vg", at 0xbec248, in main_construct(int, char**)
      Source "src/subcommand/construct_main.cpp", line 342, in main_construct [0xbec248]
#4    Object "/Data/program/vg/bin/vg", at 0xeb7e6c, in vg::Constructor::construct_graph(std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::vector<vcflib::VariantCallFile*, std::allocator<vcflib::VariantCallFile*> > const&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>)
      Source "src/constructor.cpp", line 2041, in construct_graph [0xeb7e6c]
#3    Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e0bc81, in __assert_fail
      Source "/build/glibc-Cl5G7W/glibc-2.23/assert/assert.c", line 101, in __assert_fail [0x7ffa46e0bc81]
#2    Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e0bbd6, in __assert_fail_base
      Source "/build/glibc-Cl5G7W/glibc-2.23/assert/assert.c", line 92, in __assert_fail_base [0x7ffa46e0bbd6]
#1    Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e15029, in abort
      Source "/build/glibc-Cl5G7W/glibc-2.23/stdlib/abort.c", line 89, in abort [0x7ffa46e15029]
#0    Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e13428, in raise
      Source "../sysdeps/unix/sysv/linux/raise.c", line 54, in raise [0x7ffa46e13428]

Is there anything that I can try?

glennhickey commented 5 years ago

There's probably a sequence name in a VCF it can't find in your fasta. Running with the latest release (1.13.0) should give you a more useful error message.

On Tue, Jan 8, 2019 at 12:15 AM tahuh notifications@github.com wrote:

Please describe: Hi

I'm trying subcommand "construct" using reference sequence VCF files that I using is COSMIC's coding/non-coding variants from COSMIC v87 data and dbSNP 150 Also I tried using insertion sequence list from those VCF files. The command I used is shown below

vg construct -r /Data/reference/hg38.fa -v /Data/reference/CosmicCodingMuts_v87.vcf -v /Data/reference/CosmicNonCodingVariants_v87.vcf -v /Data/reference/dbsnp150.vcf.gz -I /Data/reference/hg38_vg_insersion_cosmic_coding_non_coding_dbsnp150.fa > hg38.vg

The error message vg sent me is written below

vg: src/constructor.cpp:2041: void vg::Constructor::construct_graph(const std::vector<FastaReference>&, const std::vector<vcflib::VariantCallFile>&, const std::vector<FastaReference*>&, std::function<void(vg::Graph&)>): Assertion `reference_for.count(fasta_contig)' failed. ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_ktaDns/stacktrace.txt

Error stack is shown below

Crash report for vg v1.12.1-113-g5c08133 "Parolise" Stack trace (most recent call last):

10 Object "", at 0xffffffffffffffff, in

9 Object "/Data/program/vg/bin/vg", at 0x792c18, in _start

8 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46dfe82f, in __libc_start_main

  Source "../csu/libc-start.c", line 291, in __libc_start_main [0x7ffa46dfe82f]

7 Object "/Data/program/vg/bin/vg", at 0x6dc48b, in main

  Source "src/main.cpp", line 68, in main [0x6dc48b]

6 Object "/Data/program/vg/bin/vg", at 0xbb2937, in vg::subcommand::Subcommand::operator()(int, char**) const

| Source "src/subcommand/subcommand.cpp", line 72, in operator()
  Source "/usr/include/c++/5/functional", line 2267, in operator() [0xbb2937]
   2264:     {
   2265:       if (_M_empty())
   2266:    __throw_bad_function_call();
  >2267:       return _M_invoker(_M_functor, std::forward<_ArgTypes>(__args)...);
   2268:     }
   2269:
   2270: #if __cpp_rtti

5 Object "/Data/program/vg/bin/vg", at 0xbec248, in main_construct(int, char**)

  Source "src/subcommand/construct_main.cpp", line 342, in main_construct [0xbec248]

4 Object "/Data/program/vg/bin/vg", at 0xeb7e6c, in vg::Constructor::construct_graph(std::vector<FastaReference, std::allocator<FastaReference> > const&, std::vector<vcflib::VariantCallFile, std::allocator<vcflib::VariantCallFile> > const&, std::vector<FastaReference, std::allocator<FastaReference> > const&, std::function<void (vg::Graph&)>)

  Source "src/constructor.cpp", line 2041, in construct_graph [0xeb7e6c]

3 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e0bc81, in __assert_fail

  Source "/build/glibc-Cl5G7W/glibc-2.23/assert/assert.c", line 101, in __assert_fail [0x7ffa46e0bc81]

2 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e0bbd6, in __assert_fail_base

  Source "/build/glibc-Cl5G7W/glibc-2.23/assert/assert.c", line 92, in __assert_fail_base [0x7ffa46e0bbd6]

1 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e15029, in abort

  Source "/build/glibc-Cl5G7W/glibc-2.23/stdlib/abort.c", line 89, in abort [0x7ffa46e15029]

0 Object "/lib/x86_64-linux-gnu/libc-2.23.so", at 0x7ffa46e13428, in raise

  Source "../sysdeps/unix/sysv/linux/raise.c", line 54, in raise [0x7ffa46e13428]

Is there anything that I can try?

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tahuh commented 5 years ago

@glennhickey Thanks to your advice and I retried construct command

The problem was CHROM field of VCF file I have did not have matched FASTA name on reference so I changed VCF's CHROM field as you said and it worked.

Thanks for your suggestion.

tahuh commented 5 years ago

Hi I thought the program went well but errors again raised when construct. Currently I am using vg release version 1.13.0 (did not compiled by myself).

command line that I typed is same as above

Before running construct I have changed chromosome name field of VCF files to our reference FASTA reference name which starts with "chr" but VCF wasn't.

Our reference FASTA was downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/ dbSNP file was downloaded from https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi with build 150 Other variant info are downloaded from COSMIC downloads page https://cancer.sanger.ac.uk/cosmic/download with current release (v87)

Below is error message

Crash report for vg v1.13.0 "Moschiano"
Stack trace (most recent call last):
#10   Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x4c4508, in _start
#9    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x175f329, in __libc_start_main
#8    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x175f135, in generic_start_main
#7    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x409dfb, in main
#6    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x8e3417, in vg::subcommand::Subcommand::operator()(int, char**) const
#5    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x91b4e8, in main_construct(int, char**)
#4    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xa39f27, in vg::Constructor::construct_graph(std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::vector<vcflib::VariantCallFile*, std::allocator<vcflib::VariantCallFile*> > const&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>)
#3    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xa38a1a, in vg::Constructor::construct_graph(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, FastaReference&, vg::VcfBuffer&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>)
#2    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xa35550, in vg::Constructor::construct_chunk(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<vcflib::Variant, std::allocator<vcflib::Variant> >, unsigned long) const
#1    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xd0e3c0, in vcflib::Variant::parsedAlternates(bool, bool, bool, float, float, float, float, float, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
#0    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xd251b2, in CSmithWatermanGotoh::Align(unsigned int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)

Also I observed many warning message like below

warning:[vg::Constructor] Skipping duplicate variant with hash d8defd50671e2ae6ffe952691cf116962d12a0ae at chr7:48645511

Is it normal?

Our server system equipped with Ubuntu 16.04 LTS and gcc 5.4.0

If you need more information please let me know.

Many thanks!

tahuh commented 5 years ago

I also omitted dbSNP150 file but keep crashing with Signal 11 error with error stacktrace below

Crash report for vg v1.13.0 "Moschiano"
Stack trace (most recent call last):
#10   Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x4c4508, in _start
#9    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x175f329, in __libc_start_main
#8    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x175f135, in generic_start_main
#7    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x409dfb, in main
#6    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x8e3417, in vg::subcommand::Subcommand::operator()(int, char**) const
#5    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0x91b4e8, in main_construct(int, char**)
#4    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xa39f27, in vg::Constructor::construct_graph(std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::vector<vcflib::VariantCallFile*, std::allocator<vcflib::VariantCallFile*> > const&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>)
#3    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xa38a1a, in vg::Constructor::construct_graph(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, FastaReference&, vg::VcfBuffer&, std::vector<FastaReference*, std::allocator<FastaReference*> > const&, std::function<void (vg::Graph&)>)
#2    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xa35550, in vg::Constructor::construct_chunk(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<vcflib::Variant, std::allocator<vcflib::Variant> >, unsigned long) const
#1    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xd0e3c0, in vcflib::Variant::parsedAlternates(bool, bool, bool, float, float, float, float, float, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
#0    Object "/Data/cfDNA_Source_Develope/linamp_strategy_with_spliced_tubes/pear/indels/vg", at 0xd251b2, in CSmithWatermanGotoh::Align(unsigned int&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)

It went well without any VCF files specified and any -I option.

Is there any reason also?